VMD-L Mailing List

From: Jian Dai (djpittdj_at_gmail.com)
Date: Fri May 08 2009 - 01:22:22 CDT

Hi, all:
I'm doing analysis of water density above cholesterols in a lipid bilayer.
Now I want to average the isosurfaces of water above all the cholesterol
molecules in a frame, how can I do that?

I was able to use "volmap density $selection -weight mass -o output.dx" to
generate the dx file of water above individual cholesterols within a box and
the command I used is like:
"water and abs(x-$O6_x) <= $cutoff and abs(y-$O6_y) <= $cutoff and z >=
$sys_c_z and (z-$O6_z) >= 0. and (z-$O6_z) <= $cutoff"", where cutoff = 10
(Angstrom), and O6_x is the x position of a specific cholesterol oxygen,
sys_c_z is the calculated z value of the center of the box.

But the grid size is different for every cholesterol. In order to average
over these data, I expect to have the same grid size for water molecules
above each cholesterol. Is there a way?

Thanks.

Jian